Water exit pathways and proton pumping mechanism in B-type cytochrome c oxidase from molecular dynamics simulations

Abstract

Cytochrome c oxidase (CcO) is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. While proton uptake channels as well as water exit channels have been identified for A-type CcOs, the means by which water and protons exit B-type CcOs remain unclear. In this work, we investigate potential mechanisms for proton transport above the dinuclear center (DNC) in ba3-type CcO of Thermus thermophilus. Using long-time scale, all-atom molecular dynamics (MD) simulations for several relevant protonation states, we identify a potential mechanism for proton transport that involves propionate A of the active site heme a3 and residues Asp372, His376 and Glu126II, with residue His376 acting as the proton-loading site. The proposed proton transport process involves a rotation of residue His376 and is in line with experimental findings. We also demonstrate how the strength of the salt bridge between residues Arg225 and Asp287 depends on the protonation state and that this salt bridge is unlikely to act as a simple electrostatic gate that prevents proton backflow. We identify two water exit pathways that connect the water pool above the DNC to the outer P-side of the membrane, which can potentially also act as proton exit transport pathways. Importantly, these water exit pathways can be blocked by narrowing the entrance channel between residues Gln151II and Arg449/Arg450 or by obstructing the entrance through a conformational change of residue Tyr136, respectively, both of which seem to be affected by protonation of residue His376.

Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field

“…The CcO model that was employed for molecular dynamics simulations in Ref. [1] is based on the high resolution (1.8 Å) X-ray crystal structure of the ba 3 -type CcO from Thermus thermophilus in the reduced state in lipidic cubic phase (LCP) crystal as obtained from the Protein Data Bank (PDB: 3S8F ) [2] . This crystal structure contains two oxygen atoms between the Fe and Cu centers of the DNC, which have been proposed to be a bridging hydroperoxide [3] .…”

“…The data provided in this article were generated for molecular dynamics (MD) simulations of ba 3 -type cytochrome c oxidase (CcO) of Thermus thermophilus [1] . Atomic coordinate data of cluster models of CcO cofactors are provided in XYZ coordinate format and atomic coordinate data of the entire CcO model embedded in POPC lipid bilayer and solvated with TIP3P water molecules and counterions are provided in PDB file format.…”

Photosystem II and terminal respiratory oxidases molecular machines operating in opposite directions

“…Based on the site-direct mutagenesis it is concluded that in the B type cytochrome oxidases, there is only one functioning entry channel for the uptake of both scalar and vectorial protons, the K-channel (154). For the proton transfer above the BNC of the ba 3 oxidase from T. thermophilus, a potential mechanism is proposed which involves the A propionate of heme a 3 , and the D372, H376, and E126 residues (155).…”

“…The computational study suggests that the PLS is a cluster rather than a single residue (307) consisting of the A and D propionates of heme a 3 and nearby residues (e.g. Asp 52 and Lys171 © 1996-2017 in the bovine COX) (155). For the B family member, the ba 3 -type cytochrome oxidase, theoretical analysis suggests that the proton transfer above the BNC involves the A-propionate of heme a 3 and D372, H376 and E126 residues, with the H376 residue acting as the PLS (155) The exact path of the pumped proton above the E286 residue is not known.…”

“…Asp 52 and Lys171 © 1996-2017 in the bovine COX) (155). For the B family member, the ba 3 -type cytochrome oxidase, theoretical analysis suggests that the proton transfer above the BNC involves the A-propionate of heme a 3 and D372, H376 and E126 residues, with the H376 residue acting as the PLS (155) The exact path of the pumped proton above the E286 residue is not known. The proton pathway from E286 towards the BNC and to the PLS is believed to be formed by a chain of temporary water molecules (302)(303)308).…”